<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="#000000" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Dear Quentin<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">This can’t be accomplished just by a change of the docker file. The configure command for the plumed build in the CP2K toolchain has to be changed too. I just applied such a change in my personal fork of the current CP2K master version (see <a href="https://github.com/mkrack/cp2k"> https://github.com/mkrack/cp2k</a>):<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><o:p></o:p></span></span></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><a href="https://github.com/cp2k/cp2k/commit/cbe099e098ced65b0aeda353db8eb4c5e391f27f"><span lang="EN-GB"><span lang="EN-GB">https://github.com/cp2k/cp2k/commit/cbe099e098ced65b0aeda353db8eb4c5e391f27f</span></span></a></span><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">You can do the same in your personal fork of CP2K and then use the URL of that github repository in one of the master_* docker files for the “git clone” command. <o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">HTH<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Quentin Pessemesse <q.pessemesse@gmail.com><br> <b>Date: </b>Thursday, 9 November 2023 at 16:19<br> <b>To: </b>cp2k@googlegroups.com <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:19486] Memory Leak on CP2k 9.1<o:p></o:p></span></p> </div> <p style="margin-left:36.0pt">Dear Matthias, <o:p></o:p></p> <p style="margin-left:36.0pt">Do you know if there is a easy way to use plumed modules beyond the default ones with these docker images ? Some modules I need are deactivated by default. I have no experience in editing docker images, and this may rather be a question for the plumed forum...<o:p></o:p></p> <p style="margin-left:36.0pt">Thank you again,<o:p></o:p></p> <p style="margin-left:36.0pt">Q.<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On 09/11/2023 15:57, Krack Matthias wrote:<o:p></o:p></span></p> </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Dear Quentin</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">I am glad to read that you could solve the problems by using the provided container images.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">For future reference, I would like the mention that the README and the docker files for CP2K production containers have been moved to a separate repository on GitHub called <a href="https://github.com/cp2k/cp2k-containers">cp2k-containers</a>, recently. Therefore, the links in my previous mail are no longer valid. The CP2K production containers can be download from DockerHub <a href="https://hub.docker.com/r/cp2k/cp2k/tags/">here</a>.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <b><span style="font-size:11.0pt">From: </span></b><span style="font-size:11.0pt"><a href="mailto:cp2k@googlegroups.com">cp2k@googlegroups.com</a> <a href="mailto:cp2k@googlegroups.com"><cp2k@googlegroups.com></a> on behalf of Quentin Pessemesse <a href="mailto:q.pessemesse@gmail.com"><q.pessemesse@gmail.com></a><br> <b>Date: </b>Thursday, 9 November 2023 at 15:33<br> <b>To: </b>cp2k <a href="mailto:cp2k@googlegroups.com"><cp2k@googlegroups.com></a><br> <b>Subject: </b>Re: [CP2K:19485] Memory Leak on CP2k 9.1<o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Dear Matthias, <o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Thank you very much for your help, we were able to solve the memory leak issue by using the mpi that is compiled with the image, with some modifications to the command you provided to account for specificities of the cluster.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Best,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Quentin<o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Le vendredi 6 octobre 2023 à 15:16:09 UTC+2, Krack Matthias a écrit :<o:p></o:p></span></p> </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Quentin</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">These containers are built differently following the usual cp2k toolchain installation process. There is no </span><span style="font-size:11.0pt">/opt/cp2k-toolchain/</span><span lang="EN-US" style="font-size:11.0pt"> folder but the folder /opt/cp2k/tools/toolchain/install/. There is no need, however, to source that setup file, because the <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/Dockerfile.2023.2_mpich_generic_psmp#L83" target="_blank"> entrypoint.sh</a> script takes already care of that. You should be able to run the container as described in the <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md" target="_blank"> READ.me</a>.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <b><span style="font-size:11.0pt">From: </span></b><span class="MsoHyperlink"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span><span style="font-size:11.0pt"> <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>> on behalf of Quentin Pessemesse <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:q.pess...@gmail.com"><u><span style="color:blue">q.pess...@gmail.com</span></u></a></span></span>><br> <b>Date: </b>Friday, 6 October 2023 at 14:59<br> <b>To: </b>cp2k <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>><br> <b>Subject: </b>Re: [CP2K:19312] Memory Leak on CP2k 9.1<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Dear Matthias, <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Thank you kindly for your advice, I will try these different versions as soon as possible.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">I've built the docker image for an openmpi version of CP2k on the cluster. With version 2023.1, I used to source the environment variables using " source /opt/cp2k-toolchain/install/setup". This does not work anymore. Is it a problem on the image's end or on the cluster end ?<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Best,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Quentin<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Le vendredi 6 octobre 2023 à 11:27:26 UTC+2, Krack Matthias a écrit :<o:p></o:p></span></p> </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi Quentin</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">There are some more cp2k 2023.2 docker containers for <a href="https://github.com/mkrack/cp2k/tree/master/tools/docker/production" target="_blank"> <u><span style="color:blue">production</span></u></a> available (build with MPICH or OpenMPI) which can also be pulled with apptainer (see <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md" target="_blank"> <u><span style="color:blue">READ.me</span></u></a> for details). Maybe, you have more luck with one of these.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <b><span style="font-size:11.0pt">From: </span></b><span class="MsoHyperlink"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span><span style="font-size:11.0pt"> <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>> on behalf of Quentin Pessemesse <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:q.pess...@gmail.com"><u><span style="color:blue">q.pess...@gmail.com</span></u></a></span></span>><br> <b>Date: </b>Friday, 6 October 2023 at 10:47<br> <b>To: </b>cp2k <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>><br> <b>Subject: </b>Re: [CP2K:19310] Memory Leak on CP2k 9.1<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Dear all, <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">The cluster staff has moved to using a docker with a CP2k image, with CP2k 2023.1 (<a href="https://hub.docker.com/r/cp2k/cp2k/tags" target="_blank"><u><span style="color:blue">https://hub.docker.com/r/cp2k/cp2k/tags</span></u></a>). The program experiences serious memory leaks (out-of-memory crash after less than 24 hours on AIMD with a system less than 100 atoms with 256 GB). The cluster cannot use intelmpi versions older than intelmpi 20. Is there a more recent version of CP2k which is stable and does not experience this type of large memory leaks?<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">We've tried to compile our own versions of CP2k with multiple versions of openMPI to no avail. The only stable CP2k version we have is CP2k 6.1, which is used with intelMPI 18 but it is on a legacy container where no new software can be installed.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Has anyone managed to use this docker image succesfully, and if so, which MPI package/version have you used ? If necessary, we can downgrade down to CP2k 9.1.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Best,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Quentin<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Le mercredi 5 octobre 2022 à 13:19:26 UTC+2, Krack Matthias (PSI) a écrit :<o:p></o:p></span></p> </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi Quentin</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">It seems that you are using OpenMPI which is known to have leaks in some versions. Check <a href="https://github.com/cp2k/cp2k/issues/1830#issuecomment-1012561166" target="_blank"> <u><span style="color:blue">this issue</span></u></a> and <a href="https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ" target="_blank"> <u><span style="color:blue">this discussion</span></u></a> here on this forum for further information.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <b><span style="font-size:11.0pt">From: </span></b><span style="font-size:11.0pt">"<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>" <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>> on behalf of Quentin Pessemesse <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:q.pess...@gmail.com"><u><span style="color:blue">q.pess...@gmail.com</span></u></a></span></span>><br> <b>Reply to: </b>"<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>" <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>><br> <b>Date: </b>Wednesday, 5 October 2022 at 12:39<br> <b>To: </b>"<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>" <<span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp...@googlegroups.com"><u><span style="color:blue">cp...@googlegroups.com</span></u></a></span></span>><br> <b>Subject: </b>[CP2K:17807] Memory Leak on CP2k 9.1<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Dear all, <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Our group is encountering a memory leak issue that makes running DFT-MD impossible with large systems (~100 atoms) on one of the clusters we have access to, even though the same calculations run correctly on other machines.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">The cluster support sent me the following valgrind output and asked me to find suggestions on how to proceed. Does anyone have input on how to deal with such memory leaks ?<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Best,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">Quentin P.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">==62== Invalid write of size 4 ==62== at 0x1EA9887: grid_ref_create_task_list (in /ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp) ==62== by 0x1E7A772: grid_create_task_list (in /ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp) ==62== by 0x1E790B3: __grid_api_MOD_grid_create_task_list (grid_api.F:938) ==62== by 0x104AA67: __task_list_methods_MOD_generate_qs_task_list (task_list_methods.F:623) ==62== by 0xF58353: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:187) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) ==62== by 0xCE087E: __qs_force_MOD_qs_forces (qs_force.F:212) ==62== by 0xCE4349: __qs_force_MOD_qs_calc_energy_force (qs_force.F:117) ==62== by 0x9AE2C0: __force_env_methods_MOD_force_env_calc_energy_force (force_env_methods.F:271) ==62== by 0x50CD0C: __md_run_MOD_qs_mol_dyn_low (md_run.F:372) ==62== by 0x50DCF2: __md_run_MOD_qs_mol_dyn (md_run.F:153) ==62== Address 0x26d18670 is 16 bytes before a block of size 10 free'd ==62== at 0x4C35FAC: free (vg_replace_malloc.c:538) ==62== by 0x2B73E68: __offload_api_MOD_offload_timeset (offload_api.F:137) ==62== by 0x2B60EDA: __timings_MOD_timeset_handler (timings.F:278) ==62== by 0x2BE2C6D: __message_passing_MOD_mp_waitany (message_passing.F:4597) ==62== by 0x2963EA5: __realspace_grid_types_MOD_rs_pw_transfer_distributed (realspace_grid_types.F:1439) ==62== by 0x2966559: __realspace_grid_types_MOD_rs_pw_transfer (realspace_grid_types.F:711) ==62== by 0xC9310B: __qs_collocate_density_MOD_calculate_rho_core (qs_collocate_density.F:966) ==62== by 0xF57698: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:109) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) ==62== by 0xCE087E: __qs_force_MOD_qs_forces (qs_force.F:212) ==62== by 0xCE4349: __qs_force_MOD_qs_calc_energy_force (qs_force.F:117) ==62== Block was alloc'd at ==62== at 0x4C34DFF: malloc (vg_replace_malloc.c:307) ==62== by 0x2F21116: _gfortrani_xmallocarray (memory.c:66) ==62== by 0x2F1C271: _gfortran_string_trim (string_intrinsics_inc.c:167) ==62== by 0x2B73E1C: __offload_api_MOD_offload_timeset (offload_api.F:137) ==62== by 0x2B60EDA: __timings_MOD_timeset_handler (timings.F:278) ==62== by 0x2BE2C6D: __message_passing_MOD_mp_waitany (message_passing.F:4597) ==62== by 0x2963EA5: __realspace_grid_types_MOD_rs_pw_transfer_distributed (realspace_grid_types.F:1439) ==62== by 0x2966559: __realspace_grid_types_MOD_rs_pw_transfer (realspace_grid_types.F:711) ==62== by 0xC9310B: __qs_collocate_density_MOD_calculate_rho_core (qs_collocate_density.F:966) ==62== by 0xF57698: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:109) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) <o:p></o:p></span></p> </div> </div> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp2k+uns...@googlegroups.com"><u><span style="color:blue">cp2k+uns...@googlegroups.com</span></u></a></span></span>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/4d753954-6ada-4d19-9092-931469136f8en%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> <u><span style="color:blue">https://groups.google.com/d/msgid/cp2k/4d753954-6ada-4d19-9092-931469136f8en%40googlegroups.com</span></u></a>.<o:p></o:p></span></p> </div> </div> </blockquote> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span 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</div> </div> </blockquote> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <span class="MsoHyperlink"><span style="font-family:"Calibri",sans-serif"><a href="mailto:cp2k+uns...@googlegroups.com"><u><span style="color:blue">cp2k+uns...@googlegroups.com</span></u></a></span></span>.<o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span style="font-size:11.0pt">To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/f282de9c-e731-4232-838c-96139638c9bcn%40googlegroups.com?utm_medium=email&utm_source=footer" 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